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Nextstrain
Real-time tracking of pathogen evolution
About usAbout us
An open-source project to harness the scientific and public health potential of pathogen genome data
Core pathogensCore pathogens
Continually updated views of a range of pathogens maintained by the Nextstrain team
SARS-CoV-2SARS-CoV-2
Up-to-date analyses and a range of resources for SARS-CoV-2, the virus responsible for COVID-19 disease
Open source toolingOpen source tooling
Bioinformatic workflows, analysis tools and visualization apps for use by the community
NextcladeNextclade
In-browser phylogenetic placement, clade assignment, mutation calling and sequence quality checks
Nextstrain GroupsNextstrain Groups
Datasets and narratives shared by research labs, public health entities and others

Featured analyses

SARS-CoV-2
the Nextstrain team
Ongoing evolution and spread of SARS-CoV-2
Mpox in the DRC
inrb-mpox
INRB analysis of ongoing mpox clade I outbreak in the DRC
H5N1 cattle outbreak
the Nextstrain team
Influenza H5N1 cattle outbreak in the USA (genotype B3.13)
HPAI outbreak
moncla-lab on GitHubnarrative
Highly pathogenic avian influenza in North America
Seasonal influenza
the Nextstrain team
Seasonal influenza evolution and antigenic drift
Mpox
the Nextstrain team
Evolution and spread of mpox clades I and II
SARS-CoV-2 lineages
the Nextstrain team
Nextclade reference tree of SARS-CoV-2 Pango lineages
SARS-CoV-2 forecasts
the Nextstrain team
SARS-CoV-2 clade and lineage frequency dynamics
Avian influenza
the Nextstrain team
Avian influenza A/H5N1 evolution and spread
Avian influenza (D1.1)
the Nextstrain team
Genomic analysis of avian influenza H5N1 (D1.1 genotype)
Oropouche
the Nextstrain team
Oropouche virus evolution and spread
Lassa
the Nextstrain team
Lassa virus evolution and spread
Yersinia pestis
ktmeaton on GitHub
Historical analysis of geographic spread of plague
Measles
the Nextstrain team
Measles virus evolution and spread
Mumps
the Nextstrain team
Mumps virus evolution and spread
Rubella
the Nextstrain team
Rubella virus evolution and spread
RSV
the Nextstrain team
RSV evolution and spread
Ebola in the DRC
inrb-drc on GitHub
Genomic epidemiology of the 2018-20 Ebola epidemic in DRC
WNV in the Americas
the Nextstrain teamnarrative
Analysis of twenty years of West Nile virus spread in the Americas
Chikungunya
ViennaRNA
Molecular epidemiology of Chikungunya virus
HIV
LANL-HIV-DB
Genetic diversity of HIV Env
Rabies
the Nextstrain team
Rabies virus evolution and spread
Yellow Fever
the Nextstrain team
Yellow fever virus evolution and spread
HMPV
the Nextstrain team
Human metapneumovirus evolution and spread

Philosophy

Pathogen Phylogenies

In the course of an infection and over an epidemic, pathogens naturally accumulate random mutations to their genomes. This is an inevitable consequence of error-prone genome replication. Since different genomes typically pick up different mutations, mutations can be used as a marker of transmission in which closely related genomes indicate closely related infections. By reconstructing a phylogeny we can learn about important epidemiological phenomena such as spatial spread, introduction timings and epidemic growth rate.

Actionable Inferences

However, if pathogen genome sequences are going to inform public health interventions, then analyses have to be rapidly conducted and results widely disseminated. Current scientific publishing practices hinder the rapid dissemination of epidemiologically relevant results. We thought an open online system that implements robust bioinformatic pipelines to synthesize data from across research groups has the best capacity to make epidemiologically actionable inferences.

This Website

This website aims to provide a real-time snapshot of evolving pathogen populations and to provide interactive data visualizations to virologists, epidemiologists, public health officials and citizen scientists. Through interactive data visualizations, we aim to allow exploration of continually up-to-date datasets, providing a novel surveillance tool to the scientific and public health communities.

Future Directions

Nextstrain is under active development and we have big plans for its future, including visualization, bioinformatics analysis and an increasing number and variety of datasets. If you have any questions or ideas, please contact us.

A bioinformatics and data viz toolkit

Nextstrain provides an open-source toolkit enabling the bioinformatics and visualization you see on this site. Tweak our analyses and create your own using the same tools we do. We aim to empower the wider genomic epidemiology and public health communities.

All source code is freely available under the terms of the GNU Affero General Public License. Screenshots may be used under a CC-BY-4.0 license and attribution to nextstrain.org must be provided.

This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, Josh Batson, David Blazes, Jesse Bloom, Peter Bogner, Anderson Brito, Matt Cotten, Ana Crisan, Tulio de Oliveira, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Nate Grubaugh, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Duncan MacCannell, Erick Matsen, Sebastian Maurer-Stroh, Placide Mbala, Danny Park, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Cecile Viboud for comments, suggestions and data sharing.

Nextstrain is supported by

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